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[WIP] OpenMMToolsMCEngine #1041

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[WIP] OpenMMToolsMCEngine #1041

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3a75a85
Add first draft of OpenMMToolsMCEngine
dwhswenson Jul 28, 2021
4290267
serialization, docstrings, mdtraj integration
dwhswenson Jul 31, 2021
d3b0537
start to tests on OpenMMToolsMCEngine
dwhswenson Jul 31, 2021
f4bcfd1
first few tests working
dwhswenson Jul 31, 2021
9942f71
more tests
dwhswenson Jul 31, 2021
311586e
that makes full test coverage!
dwhswenson Jul 31, 2021
a66b3e5
fix to tests when openmmtools not available
dwhswenson Jul 31, 2021
c2b51a5
copy openmmtools dicts when deserializing
dwhswenson Aug 2, 2021
4ee3d8b
add support for any kind of mover; more tests
dwhswenson Aug 3, 2021
207c0fb
Everything except last bits of example
dwhswenson Aug 4, 2021
116a9db
some cleanup to get the engine to run in example
dwhswenson Aug 7, 2021
e94fb60
update MC engine example
dwhswenson Aug 11, 2021
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copy openmmtools dicts when deserializing 
See choderalab/openmmtools#517
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@dwhswenson
dwhswenson committed Aug 2, 2021
commit c2b51a51eeb48f1533b0be715c5ca074ea412b8f
5 changes: 4 additions & 1 deletion openpathsampling/engines/openmm/mcengine.py
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Expand Up @@ -140,7 +140,10 @@ def to_dict(self):

@classmethod
def from_dict(cls, dct):
deserialize = openmmtools.utils.deserialize
# deserialize = openmmtools.utils.deserialize
def deserialize(entry):
entry = copy.copy(entry)
return openmmtools.utils.deserialize(entry)
dct['thermodynamic_state'] = deserialize(dct['thermodynamic_state'])
dct['move'] = deserialize(dct['move'])
return cls(**dct)
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2 changes: 0 additions & 2 deletions openpathsampling/tests/test_openmm_mcengine.py
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Expand Up @@ -129,8 +129,6 @@ def test_serialization_cycle(self, mcengine):
serialized = mcengine.to_dict()
deserialized = mcengine.__class__.from_dict(copy.copy(serialized))
reserialized = deserialized.to_dict()
pytest.skip()
# this assertion currently fails: see choderalab/openmmtools#517
assert serialized == reserialized

def test_mdtraj_topology_error(self, mcengine):
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